When did Doctor Manhattan every show the ability to alter reality? If he did, the conclusion of Watchmen was totally unnecessary.

I have the feeling you have made the point here as to what 'The Doomsday Clock' will be based around. I have spoken on this subject Before, but when you look to the way the New-52 reboot was structured the Flashpoint events revision of reality replaced the strength and prescence of Superman in the universe with a weaker, less able incarnation of Superman. The lack of any inner conviction and inner strength to this new Superman was tangible.
Whether this was Doctor Manhattan's doing, whether it was he who created this Superman to take the originals place, is not altogether clear, evidence so far suggests it was, and if so then based on the return of the original Man of Steel via Convergence and what led up to the rapid realigning of the DC earth with his return and the Rebirth event, culminating in the conclusion to the recent Mr Mxyzptlk storyline, shows in no uncertain terms just how potent and formidable the existence of Superman is to the Universe.

If you accept the theory that Manhattan created the New-52 Superman to replace the problematic original, and therefore eaase the restructuring of reality to Manhattan's bleaker preferences, then the return and continuing presence of the real Superman is very likely the single biggest challenge Manhattan faces to any further attempts to bend reality once more. If Superman is the metaphysical fixed point - tthe force that stabilises reality and prevents the likes of he, Dominus, Vyndxtv, The Time Trapper, and Mandrakk from over-writing it, then the problem Manhattan faces isn't so simple as a merely physical one. As what Manhattan is attempting in the DC universe isn't physical. Rather It is a metaphysical and philosophical assault on a worlds spiritual outlook and right to determine its own sense of worth.

And so this is the problem needling Doctor Manhattan... Superman. He doesn't budge easily.

Think that Superman in some real and unique sense is almost like an agent of the prsence within the DCU, almost as if just as the Spectre is to represent the Wrath of Godm he represents in some sence the hope of the DCU!

Wasn't it implied back in the PC says that the God of the DCU had chosen Him to be the ultimate Guardian of it, with that Sword of His?